actually i dont have any idea of netbeans or eclipse... how they work or compile the source..

i just saw you are working on windows.. otherwise you could have used autoconf and automake to create makefiles on linux/unix for large number of files.. thats a very easy process.. but i dont know if automake work on windows..leave this..

which platform you compile your code with netbeans??

on windows it is easy to use visual studio but i dont know if you have visual studio?

thats all you need to do.. now if you add any new file to project, just add it to Makefile.am and aclocal to make again.
if autoconf or automake give error for any missing files, create these file using touch. it may give error for INSTALL, COPYING, README, NEWS, depcomp, AUTHORS etc etc.. so create these files manually.